3: Those We Thought We Knew
by GrimmGirl8
Summary: Third of five. Molly finds herself in the middle of one of Sherlock's cases, with surprising results. Post Christmas Special, written before Series Four. Spoilers. Editing in progress.
1. Locked-Pub Mystery

_Sequel to "The Trial of Sherlock Holmes," and "Unexpected Beginnings."_

 _March 2015_

Molly entered the morgue just before the start of the late shift. It had been an exceedingly long week, not least due to the family of four in the motorway pile-up. But, it was almost over. Only one more day before a relaxing, three-day weekend. She had made a deal with Dr Roberts that, if she took his shift today, he would take her next two. While she had always been a bit of a pushover, as of late, her negotiating skills were getting better. Maybe it was the new haircut. Or perhaps it was repeating the words Sherlock had said to her, a little over a year ago. Whatever the reason, her confidence had grown tenfold and she was more than thankful for it.

As she pulled on her lab coat, her fingers lightly brushed the piece of paper taped to the inside of the locker. She had written those fateful words down - a constant reminder of possibly the most important thing ever said to her. _You matter. You've always mattered._

The words may not have meant what she wanted them to mean. Hell, they may have even been a lie to get what he wanted. It wouldn't be the first time. But it didn't matter. They had worked. And she had used their power to her advantage.

With a deep breath, she repeated the words once more, shutting the locker door and heading for the morgue.

As Molly Hooper took up her scalpel, she couldn't help but to sigh as she caught sight of a silver-haired man, biting at his nails in the gallery above her. She spoke a bit more loudly than usual, making sure the microphone suspended above the examination table picked up her voice through the mask.

"It won't go any faster with you hovering, Greg."

DI Lestrade looked more than frustrated as he stepped forward to hit the intercom button and reply.

"He won't answer my calls until I have an answer!"

Molly sighed again, beginning her examination.

"Still not sure why you need me. If he doesn't see any potential in the case, there's no changing his mind. You know that better than anyone."

"Yes, but there has to be something. I mean, he loves these sorts of cases! How could he not like a locked-room mystery?"

"It's not really a 'locked-room mystery', though, is it?"

"How is this not a locked-room mystery? The victim walks into the pub, seemingly fine, so far as we can tell from CCTV, then collapses at the bar and dies from a stab wound just moments later! The footage shows no one leaving or entering, from the time he left to the time police arrived. All four witnesses were interrogated at the scene. No weapon was found..."

"You've said it, though. Four witnesses. Four potential killers. Hell, they might all be in it together."

"Yes, but there was no weapon. Nothing to match the hilt mark made by the blade. We looked everywhere. Sherlock looked everywhere. And yet, he's still convinced there's nothing for him on the case. That why I need you to rule out that the weapon is still inside the wound. Show him that this really is a case he needs to be on!"

Molly didn't pause in her work, but rather gave a fleeting glance over her shoulder.

"Greg, why is this so important to you? So he's not interested in this one. What's the big deal?"

"Molly, he's not interested in anything anymore. He hasn't been over to see John and the new baby, he's barely eating, he just sits all day in his parlour, staring at that web of red string he's built himself…"

"Well, that's hardly surprising behaviour. Not for him, anyway."

"Oh yeah? Well, Mrs Hudson told me that last week she threw away one of his mouldy, disgusting 'experiments' -"

"So?"

"He thanked her for doing it."

Molly stopped dead, turning to look at the DI with wide eyes.

"You mean, he said it sarcastically?"

"No. As near as she could tell, he was being sincere. Took it upon himself to throw out a couple of human body parts, as well."

The medical examiner's brow furrowed as she continued her work.

"Alright, something is definitely wrong, then."

"Exactly. But he won't talk to me unless I have a case. And, even then, it'll be a long shot. So, please. Tell me you have something?"

"Well, the x-ray revealed a small, circular item in the abdomen, but there was no indication as to how it got there. There is definite evidence of a wound tract: organs perforated, muscles torn.… Actually, if I didn't know any better, I'd say the surrounding tissue had been frozen."

"Are you proposing that he was stabbed with an icicle? Sherlock's not going to believe that one for a moment."

Molly took a sample of tissue over to the microscope for closer examination.

"It's not about whether he 'believes' it, or not. That's what the evidence is showing. What is it he's always saying? Facts to suit theories, theories to suit facts? Now, wait a minute, what are you doing here?"

Greg excitedly slammed the button to speak.

"What is it? What did you find?"

"Well, it appears to be a bone fragment, inside the frozen tissue, but -"

She went back to the corpse to confirm her suspicions.

"- there are no splintered or fractured bones anywhere near the wound, almost as if -"

"What? 'As if' what?"

"No, it's too insane. Not possible."

"What's insane? What's not possible?"

She ignored his prompts, instead delving even further into wound. When the proper techniques proved too slow for her growing impatience, she started to dig with her gloved hand. Finally, she drew out a small, metal circle from the wound a washed it off. As she recognized the object she was holding, her voice grew as cold as the blood now running through her veins.

"Call Sherlock. Now."

"Why? What is it?"

With a deep breath, she turned, holding the object up for him to see through the window.

"My engagement ring."


	2. Mollycoddled

Sherlock burst through the doors of St Bart's, striding passed Molly and Lestrade as he headed for the morgue. While Lestrade jogged, Molly had to nearly run to keep pace.

"Are you sure? Are you absolutely positive?"

"Would I have had Greg call you if I wasn't?"

"Go over it again. What are the facts?"

"Single stab wound to the abdominal wall; entrance point 1.2 centimeters wide, penetration nearly 16.9 centimeters in depth. Evidence of internal trauma to organs and surrounding tissue causing severe and fatal exsanguination. Foreign tissues found in the wound tract, none belonging to the victim. Foreign tissues exhibit signs of being frozen, as well as containing a small, white gold metal band with multiple diamonds in the setting -"

The group had come to the morgue doors, which Sherlock violently threw open.

"And you're sure it's the one Tim gave you?"

"Tom. And yes, it may not have been a long engagement, but yes, I know my own engagement ring when I see it."

Sherlock pulled on a pair of gloves, beginning to examine the body before him.

"What did you do with it after the engagement ended? Top of your vanity? Pawn shop? Rubbish bin?"

"No, I gave it back to him. It was an amicable split, after all. Didn't seem right; keeping it."

Lestrade approached the examination table, looking down as the consulting detective pawed at the victim.

"I'm sorry, could someone please explain to me what is going on here? In English, preferably."

With a deep breath, Molly stood as straight as she could, trying to steady her nerves.

"Do you remember, at John's wedding - Sherlock was going on and on about that unsolved case? The one with the Royal Guard in the bathroom stall?"

"And then it turned out the killer was actually there at the wedding? Yes, of course I remember. Only time I've ever arrested a murderer at a wedding. Well, that I was attending, anyway."

"Do you remember the part where Sherlock asked the guests to give their theories? And then, Tom stood up -"

Greg broke into a smile and had to stop himself from laughing.

"Oh, God, yes! 'Meat dagger,' wasn't it? You were so embarrassed that you practically dragged him back into his seat. Oh, we had a good laugh about it, afterwards."

Molly, however, was not amused, staring at the DI with a grave look. The bemusement soon dropped from Greg's face, replaced with realisation, and then disbelief.

"What? No, it can't be. Don't be daft. It might not have ended well between you two, but Tom would never - I mean, he was such a nice guy!"

"Well, besides that fact that, as Sherlock so helpfully put it, I do seem to fall for sociopaths -"

The aforementioned man failed to suppress a chuckle, angering Molly all the more.

"Unless Tom is the world's best actor, there is no way he's capable of this!"

Greg was now the one to raise his voice.

"Well, obviously, he is, Molly! The evidence is kind of hard to disput! I mean, let's be rational -"

Sherlock straightened, pulling the rubber gloves from his hands with a snap.

"Yes, let's be rational for a moment. The evidence tells us the following: someone who knew about Tim's unfortunate 'meat dagger' theory and of Molly's connection to him, decided to prove his theory right. That narrows it down to anyone at the wedding, anyone who reads John's blog, and/or anyone who might have a grudge against Molly. Not necessarily just Tim."

"Tom."

Molly corrected her friend with a grateful sigh and a small smile. Sherlock nodded.

"Tom. Quite. Lestrade, you said there were only four people in the pub besides the victim. No one else in or out. Were any of them Tom?"

"Well, no. They weren't."

"Which means that he was either the victim of a very specific break-in that he may be unaware of, or he is in danger. Molly, do you still have his address? We shouldn't lose a moment."

Sherlock started for the door, followed closely by Lestrade and Molly.

"Yes, of course. But, it will take some time to get there. It's in Loughton."

The DI and consulting detective both stopped walking, looking at one another in realisation. Molly stopped, too, noticing that her two companions had stopped.

"What? What's wrong?"

Lestrade spoke, eyeing Molly then Sherlock.

"Loughton? Outside the Metropolitan line?"

"Well, yes. He always said he hated living in London, though I never understood why."

The two men exchanged a silent conversation, ending in a heavy sigh from Sherlock.

"Take Anderson. He's least likely to destroy the crime scene."

"Sherlock, I don't understand. Why can't you go with Greg?"

After a pause, Sherlock lifted the leg of his trousers, revealing a small, black box strapped to his leg.

"I'm on a sort of 'house-arrest.' I'm confined to the London Metropolitan Area."

Molly nodded, making a note to ask more questions later.

"Alright. Well then, Greg, I guess it's just you and me, isn't it?"

This statement took Greg aback, looking at Sherlock for some support.

"You - you want to come with me?"

"Molly, I'm not sure that's such a good idea."

"Yeah, I mean, are you sure? Not exactly your area."

"Yes. Not sure it's safe -"

"Stop! Both of you!"

She was wild-eyed and holding out both hands in hopes of silencing them. The two men did as she wished, staring at the medical examiner with great interest. With a deep sigh, she lowered her hands and spoke as calmly as she could.

"Look. I am not fragile or something to be coddled. I am not the same silly, doe-eyed, sappy, fainting girl I once was. It's about time you took me on a proper case again, and it might as well be the one that involves me."

Sherlock took a moment to process her words, then nodded at the DI. With a defeated sigh, Greg returned the nod.

"Alright. But if anything happens, you are to stay behind me and hide!"

Molly nearly squeaked with excitement at his words.

"Just, let me grab my coat, and I'll be right back!"

As she dashed through the doors and out of sight, Sherlock lowered his voice, turning to Lestrade.

"The slightest bit of danger, you get her out of there. If it means letting the suspect go, you let him go. If her ex is capable of this, he's capable of anything."

"Of course! I'd never let anything - Hang on, I thought you said that is wasn't Tom."

He gave the DI a knowing glare as Molly bounded back into the room. She wore an excited smile with her warm coat and jumper.

"Shall we, then?"

Lestrade gave Sherlock one last look, then headed for the door.

"I'll call you when we get there."

But, Molly hung back, turning to the consulting detective.

"Thank you, Sherlock."

"For what?"

She spoke softly and with complete sincerity, getting just the slightest bit closer to him.

"For being kind."

Leaving the bewildered man in the hallway, she gave him a small smile before passing Greg who held the door for her.

"Did you really faint?"

"God, it was only twice!"


	3. Saving Tom

_***In the interest of time, I will be posting this story without editing it first. Please bare with any temporary typos or grammatical errors. Thank you.***_

A little over an hour later, Molly exited the police call, following Greg up to the small house in Loughton.

"I said 'wait in the car!'"

"You're not getting rid of me that easily, Detective Inspector!"

With a growl of disapproval, he began to knock on the door.

"Tom! It's Greg. Greg Lestrade, Molly's friend?"

After a moment of silence, he tried the door.

"No answer and it's locked. Don't suppose you still have a key? Be a bit faster than a warrant."

"Yes, I do, actually. Been meaning to give it back for months, now."

"Still carrying his key around? And you sure you're over him?"

Greg began unlocking the door as Molly bristled.

"Look, it's not as if I didn't want to give the key back. I simply kept forgetting!"

The door swung open and Lestrade started in with caution.

"You know, I never did understand you two. What did you ever see in him?"

"Not exactly the time, Greg!"

"Right. Sorry. Tom? Are you here?"

No answer. The two pressed forward, making their way through the house, little by little, which only began to frustrate Molly.

"If he is in trouble, why are we moving so slowly?"

"Because we don't know who else might be here, Molly. Tom? Anyone home?"

"Look, this is ridiculous. Tom, doesn't need saving! He's probably at work. It's nearly nine, after all!"

"Do you leave for work with breakfast half eaten and still on the table?"

Looking into the kitchen, Molly gasped as she registered what she was seeing. Greg raised a hand to silently shush her, turning his gaze upstairs. Quietly, he grabbed for his gun, motioning for her to stay put, which she gladly obeyed. Every nerve in her body seemed to vibrate as she stood stock-still next to the table. Her thoughts ran wild as the prevailing silence took a toll on her worry. She nearly jumped from her own skin when her friend's voice rang through the house.

"Molly, love, go back to the car. I'll ring Sherlock. You don't need to see this."

"What is? What did you find?"

Before the DI could bar her path, she was up the stairs, passed him, and into Tom's bedroom. All at once, a cold shiver ran up her spine and seemed to choke a verbal reaction from her. The headboard of the bed had been removed from the wall and laid face-down. On the back of it, and on the wall behind, were dozens of what looked like surveillance photos. As she moved closer, Molly began to notice a chronological order. The first set were of John, seemingly a bit younger, and a little more plump than now. Then, John's horrible mustache phase. Then Mary. Then - _no, not the baby, too!_

Molly's mind began to reel as she took in photo after photo until one, in particular, made all thought come to a screeching halt. At the very top of the group was a single photograph of Molly, coming out of St Bart's and walking with John. But the army doctor wasn't the focus of the image, unlike every other pasted to the headboard. No, she was. And next to it, an article ripped from a newspaper, with her name circled in red.

Molly's breath became shallow and her heartbeat quickened. Was it all a lie? Had it all been yet another lie? After a moment of sheer panic, the medical examiner noticed that Greg had moved to the bathroom and was staring in through the open door.

"What is it? What's in there?"

"No, Molly, don't - !"

But it was too late. As Molly turned the corner, she let out a horrified and blood-curtling scream. In the bathtub, lay Tom, with a single gunshot wound to the forehead.


	4. Existential Aftermath

_***In the interest of time, I will be posting this story without editing it first. Please bare with any temporary typos or grammatical errors. Thank you.***_

Molly sat in 221B, shaking from head to toe. She just couldn't stop seeing it in her head: all those images of John, of Mary - and of her. Her name circled in some newspaper article like the victim of a hit! Is that was she was? A target? Is that all she had ever been to Tom? Just another pawn in some sicko's game?

She was so caught up in her own thoughts that she barely registered the two men behind her, speaking in the kitchen.

Lestrade had taken photos of the crime scene, and was now showing them to Sherlock.

"Again. Go over it again."

Greg sighed, lowering his voice as best he could.

"We entered the house with Molly's key. No signs of forced entry on the doors or windows. Inside looked clear with no signs of a struggle. The only thing that seemed off was the food on the table. I told Molly to wait and that's when I went upstairs and saw all this."

"And it was all laid out? Just like this?"

"I didn't touch a thing before taking those photos. It must have been planted there before we got there, but why?"

These words finally stirred Molly enough to speak from the chair.

"No. It wasn't planted."

Greg raised his voice, walking over to where he was seated.

"Molly, dear, why don't you go home. I'll have an officer -"

"No!"

She stood just as abruptly as she spoke. Her heart pounded madly in her chest as she addressed the two men.

"No, I want the truth. I want to know exactly what's going on."

With pleading eyes, she looked at Sherlock.

"It wasn't planted there, was it?"

The consulting detective sighed, but didn't break her eye contact.

"No. It wasn't. In fact, if I had to guess, I'd say he died only moments before you got there."

Molly was now fighting back tears, a flood of mixed emotions threatening to make them bubble over onto her cheeks. She remained as steadfast as she could, eyes still locked on Sherlock's.

"You need to explain. You need to tell me what all this means. And quickly."

"Then, maybe you should sit -"

"No!"

With another sigh, Sherlock started to speak in his usual quick and calculated way. Normally, this had brought great comfort to Molly; something she could always rely on at the conclusion of a case. But not today. Today, it only brought more heartache.

"Before I faked my death, Moriarty had kidnapped two children using someone who looked enough like me to scare the girl when she first saw me. Part of his plan to discredit me. I believe that Tom was that person."

Greg's eyebrows creased.

"Hang on, but you told Anderson they bumped that guy off! And that you used his body as a plant, or something, when you faked your death."

"Do you really think I would have told the truth to Anderson?"

"No. Unless, of course, you knew he wouldn't believe the truth, even if you told it to him."

Molly now practically screamed with frustration, causing two tears to fall onto her cheek.

"Please! Both of you! Sherlock, what are you saying?"

"Molly, I'm saying that Tom was a hit man. Sent to keep an eye on John after I died. And he locked onto you because you were an easy target and a way to stay close to him."

"Sherlock! You can't just say things like that to -"

"No. No, he's right. I was an easy target. A very easy target. God, I'm such a fool!"

She collapsed into a kitchen chair, tears now flowing steadily down her face. Sherlock knelt down next to his friend, trying to lend what little comfort he could.

"You are not a fool, Molly Hooper. You were taken in by a con-artist. Someone whose very life depended on lying."

"Twice! First by Jim, then by Tom! Because I'm weak and silly and easy -"

"No, Dr Hooper, because you are _strong_."

These words made her look up, Sherlock's face now only inches from hers.

"Molly, anyone can con a weak person. It's too easy to the point of fault; making it easier to slip out of the lie and back into truth. True con-artists don't target the weak, they target strength. And the fact that Tom was able to get away with it for so long is testament to exactly how strong a person you are."

Molly stared for a moment as she tried to process his words. Finally, she sniffed and gave a wet chuckle.

"That has to be the weirdest compliment I've ever been given."

Sherlock smiled and straightened, patting her on the shoulder.

"It's the truth. Now, I agree with Lestrade: it's best if you go home, get some rest. I'll send Mrs Hudson with you, just to make sure you're alright."

She nodded, standing.

"Thank you. Both of you. Truly."

Both men nodded as Molly made her way to the stairs and out of the flat.

Once he was sure Molly was out of earshot, Greg turned to Sherlock.

"So, Tom was a hitman? But he never actually went after John, only observed him. Why? What does it mean?"

Sherlock had begun to scroll through the images once again, watching his best friend's progression since his fateful jump from the roof of St Bart's to the present day. He stopped on the photos of John, Mary, and the baby leaving the hospital just one month before.

"It means that none of them are safe. No matter what I do, no matter what I don't do - No one is ever truly safe."

"Well, while you're dwelling on the existential aftermath of that statement, there's one thing last thing I wanted to show you. I was just waiting until she'd gone."

Lestrade handed Sherlock the photograph of Molly which had since been wrapped in an evidence bag. Turning it over, the consulting detective, saw a single word, scrolled on the back in bright red: consequences. Sherlock took a deep breath, instantly making the connection with that case which ended the day baby Watson had been born.

"It looks just like the one from the tea-party killer's murder, doesn't it? But, there's nothing else connecting the two -"

"May I keep this?"

"Keep - the photograph? No, Sherlock, it's evidence, you can't just…"

But the look of unyielding determination on Sherlock's face made him understand that it hadn't really been a question.

"Fine. But, if anyone asks, you didn't get it from me. Now, I have to get going. I promised John and Mary I'd pop in a little later. Call me if you make any sense of this, alright?"

"Of course, Lestrade. The very moment I do."

"Yeah. Sure you will."

With the smallest smirk, Lestrade winked and headed down the stairs.

Finally alone, Sherlock moved to the hallway door, closing it to reveal the only free bit of wall space in the entire room. The rest of the parlour had been transformed, only a few months prior, to a web of red string and Internet clippings all center around one simple phrase: did you miss me?

Now, however, it was time to start a new web of clues. Sherlock took a thumbtack from a drawer, before looking at the image of Molly for a good long moment. Finally, he faced the image to the wall, tacking the evidence bag so that only the glimmering, threatening red letters shown back at him.


	5. The Nursery

_***In the interest of time, I will be posting this story without editing it first. Please bare with any temporary typos or grammatical errors. Thank you.***_

 _Two days later_

Molly climbed the stairs of 221B, carrying two large shopping bags. Reaching the landing, however, she saw no one.

"Sherlock? You here?"

"Upstairs! John's room."

She sighed, looking at the remaining flights of steps and beginning to climb them, reluctantly.

"You know, you can't very well keep calling it 'John's room.' He's not lived here for years."

She rounded the corner to see Sherlock, sitting on the floor and surrounded by pieces of wood. Though she tried, Molly couldn't suppress a laugh.

"What on earth are you doing?"

Sherlock's face was so screwed up from confusion, the image reminded the medical examiner of a distraught pug.

"How, exactly, is one supposed to understand the instructions if there are no words? They don't even both to print the in Swedish! It's not as if it's a difficult language to learn, anyone could do it!"

"Is that - a crib?"

"Yes, of course, it's a crib! What else do you put in a nursery?"

"Your building a nursery? In John's old room? Then, why did you have me get all this?"

She opened the bags and began to take out beakers, a microscope, and several medical photo illustrations.

"Decorations, of course."

"You can't put this stuff in a baby's -"

She began to laugh again, but stopped, seeing the serious look on his face. She cleared her throat, looking down and continuing to unpack.

"Yes, quite. Quite lovely, they will look wonderful and she will love them."

Sherlock went back to his sundvik, only to be quickly frustrated to the point of a growl. Molly smiled, taking the pieces from him.

"Here. Allow me."

"Yes. Thank you."

He stepped aside and started to arrange the items she'd brought.

"So, how's it going? With the whole 'my ex-fiancé is a murdering hitman' - thing?"

"It's - well… it's made me think. I just feel like - everything I know is wrong. Every major relationship I've had has been a lie. I didn't 'move on.' If anything, I took a hundred steps back."

"If you keep talking like that, he really will have won."

Molly really did laugh now, shaking her head.

"I didn't peg you as one to spout childish rhetoric."

"I'm being serious, Molly."

She stopped, looking up to see the most serious face she'd ever seen on the man's face. He didn't move, but his eye softened as he looked at her.

"Don't let him take the one thing from you that sets you apart from who you once were."

"Oh? And what's that, then?"

"Your confidence, Molly Hooper."

The words filled her soul with such warmth, she felt as though she may cry. Instead, she turned back to her work, finding the two pieces she needed.

"Yes. Quite. So, does John know you're doing this? Making a nursery?"

"No. He doesn't."

"You haven't spoken to him since the baby was born, have you?"

"I've been giving them their space. That's what you're supposed to do with new parents, aren't you? Give them space. Besides, I've been focused on this whole Moriarty thing. Have to get him taken care of first, don't I?"

"Don't. Don't do that. Not to throw your own advice back at you… but don't let him take the one thing that sets you apart from who you once were."

He smirked.

"And that would be?"

"Your friends, Sherlock Holmes."

He cleared his throat, nodding and going back to his work.

"Yes. Well… shall we continue, then?"

She nodded, smiling to herself as she helped her friend to complete the nursery.

End.

 _Story continues with "The Nanny."_


End file.
